April 4, 2013
Because I am preparing this paper from PLOS ONE, with its stupid numbered-references system, I am finally getting to grips with a reference-management system. Specifically, Zotero, which is both free and open source, which means it can’t be taken over by Elsevier.
As a complete Zotero n00b, I’ve run into a few issues that more experienced users will no doubt find laughable. Here are two of them. I need to cite Greg Paul’s classic 1988 paper on the skeletal reconstruction of Giraffatitan:
Paul, Gregory S. 1988. The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2(3):1-14.
When I render this using Zotero’s PLOS ONE style, it comes out as:
Paul GS (1988) The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2: 1–14.
So the first problem is, how can I get Giraffatitan to be set in italics?
And the second one, which is arguably more important, is how can I get the issue number included? I undertsand that PLOS ONE referencing style omits the issue-numbers by preference, since they are often redundant, with the pages of each volume being numbered consecutively across volumes. But Hunteria is one of those journals (PaleoBios is another) that resets page-numbers at the start of each issue. As a result, Hunteria volume 2 had at least three page 14s, one in each of its issues, so that issue number is a crucial part of the reference.
Help me, SV-POW! readers — you’re my only hope.
April 3, 2013
Gah! No time, no time. I am overdue on some things, so this is a short pointer post, not the thorough breakdown this paper deserves. The short, short version: Schachner et al. (2013) is out in PeerJ, describing airflow in the lungs of Nile crocs, and showing how surprisingly birdlike croc lungs actually are. If you’re reading this, you’re probably aware of the papers by Colleen Farmer and Kent Sanders a couple of years ago describing unidirectional airflow in alligator lungs. Hang on to your hat, because this new work is even more surprising.
I care about this not only because dinosaurian respiration is near and dear to my heart but also because I was a reviewer on this paper, and I am extremely happy to say that Schachner et al. elected to publish the review history alongside the finished paper. I am also pleasantly surprised, because as you’ll see when you read the reviews and responses, the process was a little…tense. But it all worked out well in the end, with a beautiful, solid paper by Schachner et al., and a totally transparent review process available for the world to see. Kudos to Emma, John, and Colleen on a fantastic, important paper, and for opting for maximal transparency in publishing!
UPDATE the next morning: Today’s PeerJ Blog post is an interview with lead author Emma Schachner, where it emerges that open review was one of the major selling points of PeerJ for her:
Once I was made aware of the transparent peer review process, along with the fact that the journal is both open access and very inexpensive to publish in, I was completely sold. [...] The review process was fantastic. It was transparent and fast. The open review system allowed for direct communication between the authors and reviewers, generating a more refined final manuscript. I think that having open reviews is a great first step towards fixing the peer review system.
That post also links to this one, so now the link cycle is complete.
Schachner, E.R., Hutchinson, J.R., and Farmer, C.G. 2013. Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria. PeerJ 1:e60 http://dx.doi.org/10.7717/peerj.60
April 3, 2013
Just like the last time I tried to post a comment on Richard Van Noorden’s piece on open-access economics, the comment I posted has been rejected with a fatuous “This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service” message.
SERIOUSLY, NATURE PUBLISHING GROUP. HOW HARD CAN IT BE?
You will notice that neither WordPress-hosted blogs such as SV-POW!, nor Blogger-hosted blogs such as Mark Witton’s offering – nor indeed PLOS-hosted blogs such as The Integrative Paleontologists — consistently throws away perfectly good comments.
It’s 2013. There is no excuse for running a non-functional blog. None. If you aspire to be a hub of meaningful discussion, you have to make your software work right. It’s not good blowing it off with a snort and a giggle, “Oh, yeah, that happens all the time, ha ha”. It’s contemptible — worse, it’s comtemptuous of your readers and of the people who spend time and effort to provide you with free content.
Sort it out.
For anyone who cares, here is the actual comment that I tried to post:
My thanks to Richard Van Noorden and David Crotty for useful criticisms of my simple calculations.
If both sets of figures are correct — that average profit-margins for the Big Four are 36% but the average across the industry is “only” 20-30% then it’s clear that the great majority of the parasitism that currently infests academia can be laid at the doors of the Big Four.
Is the Big-Four number correct? All we have to go on is the figures that those corporations themselves publish — and those are what I used in the linked blog post. If Wiley have now changed what they report, then we can use their new number instead. What we can’t legitimately do is look at what they say they make, then use a different number of our own choosing.
And here is where we reach the real problem: the appalling lack of transparency. David Crotty rightly points out “the assumption that the entirety of the $9.4 billion brought in by the publishing industry comes from subscriptions”. But I have tried very hard to get a number for what proportion of income is indeed from subscriptions, and not been able to get answers from Big-Four publishers. One of them explicitly told me to stop even asking. In the face of such obscurity, all we can do is work with what numbers we do have.
If any of the Big Four would like to reveal the true numbers, I would be delighted to hear them, and to revise my calculations accordingly.
Meanwhile here is my least bad re-calculation. If industry average profit margins are 20-30%, we’ll use the middle of the range, 25%. That means that 1/4 of the annual $9.4 billion revenue is profit — 2.35 billion. By coincidence, this is almost exactly equal to the price of publishing the year’s 1.8 million articles as Gold OA at a PLOS ONE price-point of $1350, namely $2.43 billion. Remember, this is not saying that what we spend on subscriptions would fund 100% Gold OA. It’s saying that what we throw away as sheer profit for publishers would fund it.
If that doesn’t make anyone absolutely furious, then that person’s outrage-meter is badly in need of recalibration. We’re supposed to be doing science here, not enriching shareholders with public money.
Thanks for listening.
March 28, 2013
I was struck by this bit of prevarication in Richard Van Noorden’s new piece on open access. First the set-up:
To [Michael] Eisen, the idea that research is filtered into branded journals before it is published is not a feature but a bug: a wasteful hangover from the days of print. Rather than guiding articles into journal ‘buckets’, he suggests, they could be filtered after publication using metrics such as downloads and citations, which focus not on the antiquated journal, but on the article itself.
So far, so good. And then we have this:
Alicia Wise, from Elsevier, doubts that this could replace the current system: “I don’t think it’s appropriate to say that filtering and selection should only be done by the research community after publication,” she says.
What does the weasel-word “appropriate” mean here?
Is Alicia saying that she doesn’t think what Eisen’s saying is correct? No, if that’s what she meant, she would have said so. “I don’t think it’s right to say X” is a much stronger statement.
In fact, “not appropriate” is code for “correct, but we’d rather you didn’t say it”. When you’re six years old, your parents tell you it would not be appropriate to remark on your Auntie Griselda’s wispy moustache. That doesn’t mean the moustache isn’t there. If it wasn’t there, you wouldn’t have an issue. Your parents wouldn’t need to tell you anything. By saying it’s “not appropriate”, your parents are acknowledging that, yes, Auntie G. does have a fluffy upper lip, but that they don’t want you to draw attention to it.
And in the same way, Alicia’s quote here means “Yes, filtering and selection should be done by the community after publication, but please don’t say so. That would be inconvenient for us, since our business model consists of taking money off you in exchange for bestowing illusory prestige. We want you to collude with us in perpetuating the illusion”.
Let’s not be complicit.
March 28, 2013
My thanks for Richard Van Noorden for drawing my attention to his new piece Open access: The true cost of science publishing in Nature. I wrote a detailed comment on this article, but when I went to post it, I was told “This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service”:
This news to me. No-one at Nature thought to tell me, or anything. Their system said nothing about when I logged in, nor when I started entering my comment. Just waited till I’d finished, then trashed it.
I have no idea why I am banned. How can I have, when I’ve never received any notification?
I can only assume it’s for posting opinions that are at odds with what NPG would prefer we all thought — at least, in the absence of any actual data, that’s the best hypothesis I can come up with. Update 40 minutes later: turns out it was a glitch in the spam-filter. Richard got it fixed, and my comment is now up on the article.
Listen up, Nature Publishing Group: you will never get meaningful dialogue in your comments if you silently ban
everyone who expresses a non-party-line opinion random people for no discernable reason. You should be aspiring to be a hub of civilised discourse on these important issues, not an echo-chamber. (If you want that, you can just go and read The Scholarly Kitchen.)
Anyway: I am paranoid enough that I copied my comment before submitting it — I’ve been screwed in too many ways by too many commenting systems to trust anything but my own. So here is that comment, stripped of its context but still IMHO important.
Perhaps someone who has not been banned from commenting at Nature could post it for me?
Thanks for this useful post, Richard. I am provoked by this statement:
“Analysts estimate profit margins at 20–30% for the industry.”
Where do such low numbers come from? As is by now well known, the profit margins for the Big Four publishers (Elsevier, Springer, Wiley and Informa) are between 32.4 and 42 percent — not one of them has a margin as low as the highest end of the range you cite. Not only that, but commercial academic publishers’ profit margins continue to rise year on year.
The average profit margin among the Big Four is 36%, which means that of the $9.4 billion spent on subscriptions in 2011, $3.39 billion was simply poured down the academic drain. Note that this profit alone would be enough to pay APCs for 2.5 million PLOS ONE articles, 40% more than the world actually produced in that year.
So to spell it out, subscription profits alone would be enough to fund OA publication of ALL research, with just under a billion dollars left over to fund additional research. It’s not just idiotic that we keep paying this ludicrously inflated subscriptions, it’s iniquitous.
March 28, 2013
There’s a good, balanced piece by Stephen Pincock in the new Nature, on the question of whether early-career researchers should publish their work in open-access journals. It seems to be free to read, so take a look at Publishing: Open to possibilities.
I mention it not only because it’s a subject dear to my heart, but also because the article mentions and quotes me. (Regarding “I got quite a lot of criticism from people I respect a lot”, most of those criticisms are in the comments on this post.)
But I also feel obliged to respond to a couple of points in the article, and since it doesn’t seem to have comments enabled, a short post here seems to be appropriate.
First, there’s this quote from Rob Brooks:
Impact factors still pretty much rule. A lot of people — grant committees, administrators and even referees — can’t assess quality. All they can do is count or pseudo-quantify. They count the number of papers you’ve got and count the impact factors of the papers and make a little metric, rather than just reading the papers.
My response: are there really referees who can’t assess quality? Do we really have situations where you submit a paper for peer-review, and the referees evaluate its quality — and recommend acceptance or rejection — not on the basis of the quality of the science, but on the impact factors of other journals you’ve published in?
If that’s true, then those referees should get out of science, now. Or, no — wait — it’s too late for that. They are already out of science. But they should stop pretending to be scientists and go work in McDonald’s.
By contrast, Robert Kiley of the Wellcome Trust is a beacon of sanity:
Many funders are looking beyond a journal’s brand name. “If you come to Wellcome for a grant,” he says, “we make it clear that funding decisions are based on the intrinsic merit of the work, and not the title of the journal in which an author’s work is published.” Kiley points to the policies of the UK programme for assessing research quality, the Research Excellence Framework, which stated in July 2012 that no grant-review sub-panel “will make any use of journal impact factors, rankings, lists or the perceived standing of publishers in assessing the quality of research outputs”
Pincock then discusses the open-access citation advantage:
Whether [open access] translates into higher citation rates is up for debate. In 2010, a meta-analysis found 27 studies showing that open-access articles had more citations than papers behind paywalls — up to 600% more, depending on the field — and four that found no open-access advantage.
I would not describe that as “up for debate”. I would describe it “has been analysed in detail and the jury is in”. As noted previously here on SV-POW! and in my submission to the House of Commons, Swan’s data says that on average open-access articles are cited 2.76 times as often as non-open.
The most misleading part of the article, though, is this you-get-what-you-pay-for assertion:
According to Carl Bergstrom, an evolutionary biologist at the University of Washington in Seattle, there tends to be a positive correlation between an open-access journal’s fees and its score in a system he co-developed that rates journals according to the number of citations they receive, with citations from highly ranked journals weighted more heavily.
However, the actual results show at best an extremely weak correlation, with very wide confidence intervals. (I find it baffling that the page doesn’t give numbers for these important measures.) Someone wanting to summarise these findings in a few words would do better to state that there is essentially no correlation between influence and price.
Apart from these caveats, the article is good, and presents multiple perspectives with little bias — to Nature‘s credit. It’s well worth reading.
March 15, 2013
We’ve seen a lot of arguments recently about the RCUK open-access policy and the length of embargoes that it allows on Green OA articles under various circumstances. When is it reasonable to insist on six months? When might publishers have cause to want to stretch it out to 24 months? And so on.
The truth here is terribly simple. There is no justification for embargoes of any length on accepted manuscripts, ever. Remember that, whatever else they do, publishers do not fund research, nor peer-review. Up to the point where a manuscript is accepted for publication, they have made no contribution, and it’s nothing short of an outrage that current policies allow them any say in what happens to the work that has been done to that point.
After a paper has been accepted, then the publication process begins. That is when publishers add their own value, through copy-editing, formatting, typesetting, etc. It is perfectly reasonable that they should have some say in what happens to the final formatted papers which they have contributed to.
But that’s all. Every accepted manuscript should be immediately made freely available with no embargo.
Any publisher that argues against this policy is saying that the value they add is inadequate. Under a zero-embargo system, libraries would still subscribe to journals if they felt that the value added by publishers was worth what they charge for subscriptions. Publishers that do a good job at a good price would not be harmed. The only publishers that could conceivably suffer under such a policy are incompetent or exploitative ones. When did it become the government’s job to protect them?
[This post is a cleaned-up version of a comment that I left on a recent Times Higher Education article.]
March 14, 2013
Whenever I write a complicated document, such as my submission to the Select Committee on open access, I get Matt to do an editing pass before I finalise it. That’s always worthwhile, but I have to be careful not to just blindly hit the Accept All Changes button.
Last Tuesday Mike popped up in Gchat to ask me about sauropod neck masses. We started throwing around some numbers, derived from volumetric estimates and some off-the-cuff guessing. Rather than tell you more about it, I should just paste our conversation, minimally edited for clarity and with a few hopefully helpful links thrown in.
* R. McNeill Alexander (1985, 1989) did estimate the mass of the neck of Diplodocus, based on the old Invicta model and assuming a specific gravity of 1.0. Which was a start, and waaay better than no estimate at all. Still, let’s pretend that Mike meant “tried based on the actual fossils and what we know now about pneumaticity”.
The stuff about putting everything off until April is in there because we have a March 31 deadline to get a couple of major manuscripts submitted for an edited thingy. And we’ve made a pact to put off all other sciencing until we get those babies in. But I want to blog about this now, so I am.
Another thing Mike and I have been talking a lot about lately is the relation between blogging and paper-writing. The mode we’ve seen most often is to blog about something and then repurpose or rewrite the blog posts as a paper. Darren paved the way on this (at least in our scientific circle–people we don’t know probably did it earlier), with “Why azhdarchids were giant storks“, which became Witton and Naish (2008). Then last year our string of posts (starting here) on neural spine bifurcation in Morrison sauropods became the guts–and most of the muscles and skin, too–of our in-press paper on the same topic.
But there’s another way, which is to blog parts of the science as you’re doing them, which is what Mike was doing with Tutorial 20–that’s a piece of one of our papers due on March 31.
Along the way, we’ve talked about John Hawks’ model of using his blog as a place to keep his notes. We could, and should, do more of that, instead of mostly keeping our science out of the public eye until it’s ready to deploy (which I will always favor for certain projects, such as anything containing formal taxonomic acts).
And I’ve been thinking that maybe it’s time for me–for us–to take a step that others have already taken, and do the obvious thing. Which is not to write a series of blog posts and then decide later to turn it into a paper (I wasn’t certain that I’d be writing a paper on neural spine bifurcation until I had written the second post in that series), but to write the paper as a series of blog posts, deliberately and from the outset, and get community feedback along the way. And I think that the sauropod neck mass project is perfect for that.
Don’t expect this to become the most common topic of our posts, or even a frequent one. We still have to get those manuscripts done by the end of March, and we have no shortage of other projects waiting in the wings. And we’ll still post on goofy stuff, and on open access, and on sauropod stuff that has nothing to do with this–probably on that stuff a lot more often than on this. But every now and then there will be a post in this series, possibly written in my discretionary blogging time, that will hopefully move the paper along incrementally.
Alexander, R.M. 1985. Mechanics of posture and gait of some large dinosaurs. Zoological Journal of the Linnean Society, 83(1): 1-25.
Alexander, R.M. 1989. Dynamics of Dinosaurs and Other Extinct Giants. Columbia University Press.
- Hutchinson, J.R., Bates, K.T., Molnar, J., Allen, V., and Makovicky, P.J. 2011. A computational analysis of limb and body dimensions in Tyrannosaurus rex with implications for locomotion, ontogeny, and growth. PLoS ONE 6(10): e26037. doi:10.1371/journal.pone.0026037
- Taylor, M.P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.
- Wedel, M.J., and Taylor, M.P. In press. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. PalArch’s Journal of Vertebrate Paleontology.
- Witton, M.P., and Naish, D. 2008. A reappraisal of azhdarchid pterosaur functional morphology and paleoecology. PLoS ONE 3(5): e2271. doi:10.1371/journal.pone.0002271
March 2, 2013
The progressive RCUK policy on open access has recently come under fire, particularly from humanities scholars, for favouring Gold OA over Green. For various reasons — and I won’t, for now, go into the question of which of these reasons are and aren’t sound — they favour an approach to open access where publishers keep final versions of their papers behind paywalls, but drafts are deposited in institutional repositories (IRs) and people who want to read the paper can have access to the drafts.
It’s appealing to think that this relatively lightweight way of solving the access problem can work. Unfortunately, I’m not convinced it can, for several reasons. I’ll discuss these below, not so much with the intention of persuading people that Gold is a better approach, but with the hope that those of you who are Green advocates have seen things that I’ve missed and you’ll be able to explain why it can work after all.
1. Two-class system
Most fundamentally, I worry that Green OA creates a two-class system which I can’t approve of. It does this in two ways.
First, it necessarily creates two classes of papers: author’s draft and publishers’ final versions. These will differ in some respects, and it’s hard in general to know what those respects are. Of course pagination will differ — which means you can’t cite page-numbers reliably. But other changes are possible as well. For example, Matt and I have a paper in press now for which a whole additional figure — an important one — was added at the proofing stage. In our case, the paper will be OA anyway, but if it were not then the authors’ manuscript would be a poor substitute.
And by implication, Green OA creates two classes of researchers — a potentially harmful division between those privileged few who have the “proper” papers and an underclass who have only manuscripts. (It doesn’t help that for stupid historical reasons, our manuscripts are often butt-ugly: double-spaced, line-numbered, all the figures at the end instead of where they’re needed, etc.)
Admittedly, the two-classes-of-researcher problem is not created by Green OA: it already exists, in a worse form where the underclass doesn’t have access to any version of the paper. But whereas Gold OA solves this problem (everyone has exactly the same access to PLOS and PeerJ papers), Green doesn’t.
(To me, it’s obvious that democratising access is a good thing. But now that I’ve made the notion explicit, I can’t help the uncharitable thought that there may be those out there who want to maintain a two-class system — to retain a notion that they are “in” while others are “out”. I hope I’m wrong, and I’m certainly not accusing Green OA advocates of having this motivation. It just seems like it might be implicit in some of the broader struggles over access. Anyway, let’s not confuse this separate potential problem with access with the actual problems with Green OA I’m addressing in this post.)
2. Expense of continuing subscriptions
I find it baffling that people keep talking as though Green OA is cheaper than Gold. It isn’t, at all. As I’ve shown previously, the cost to the world of a paywalled paper (aggregated across all subscriptions) is about $5333. There is no reason to think that will change under the Green model, in which we continue to give the final and best version of our work to publishers.
By contrast, even the publisher-influenced Finch estimates typical Gold APCs as £1500-£2000 (about $2270-$3030), which amounts to 43%-57% as much. (Conveniently, the midpoint of the Finch range, £1750, is about $2650, which is almost exactly half of what we pay by the subscription model.
But the true cost of Gold OA is much, much less. Follow the link for the detail, but one credible banner figure starts with the observation that half of all Gold OA articles are published at no cost to the author and that the average APC of the other half is $906, to arrive at a true average APC of $453 — about one twelfth of the cost for a paywalled article.
So for purely pragmatic financial reasons, Green seems like a silly path. There’s a very short-term saving, sure, as we avoid paying APCs. But we have to look further ahead than the next five years.
Now there is nothing intrinsic to Green OA that means embargoes must be in place. It’s perfectly possible, and manifestly desirable, that no-embargo Green-OA mandate should be enacted, requiring that authors’ final manuscripts become available immediately on publication. But for whatever historical reasons (and I admit I find this baffling) there are few or no Green-OA mandates that do this. Even the best of them seem to allow a six-month delay; twelve months is not uncommon (and Michael Eisen worries that the new White House policy with further establish twelve months as the norm.
I will have more to say about embargoes in a subsequent post. (SPOILER: it’s not going to be pretty.) But for now it suffices to say that any system that makes research freely available only a year after it’s published is wholly inadequate. Not to mention stupid. Stupid and inadequate.
So if Green OA is going to be the solution we need, it has to break free from embargoes.
4. Non-open licences
Similarly, there is no intrinsic reason why Green OA should mean non-open licences and Gold OA should mean truly open (BOAI-compliant) open access. And yet history has brought us to a point where is often how things are. For example, the RCUK policy (even before its progressive erosion got properly under way) says of its Gold arm that “The CC-BY license should be used in this case”, but contains weasel words in its Green arm:
the journal must allow deposit of Accepted Manuscripts that include all changes resulting from peer review (but not necessarily incorporating the publisher’s formatting) in other repositories, without restrictions on non-commercial re-use.
This just won’t do. It’s not open access. To quote Heather Piwowar’s pithy statement once more, “We do basic research not only to know more, but to do more”. Non-commercial licences impede the use of research, and that’s not to the benefit of wider society. (I won’t labour this point now, because I’ll have more to say on non-commercial clauses in a subsequent post.)
So as with embargoes, if Green OA is going to be the solution we need, it has to break free to its habitual acceptance of non-commercial clauses.
5. Practical failings
On top of the fundamental problems already discussion (two-class system, expense of continuing subscriptions, embargoes and non-open licences), the repository system as it exists today suffers from a suite of practical problems that render it pretty inadequate.
- Many institutions don’t even have an IR; or if they do it doesn’t work.
- Many scholars aren’t associated with an institution and so don’t know where they should reposit their manuscripts. (That this is overlooked is a symptom of an unfortunate elitist tendency among academics.) [UPDATE 4th March: thanks to Neil Stewart, whose comment below points out Open Depot as a solution to this.]
- The use of IRs involves an institution-by-institution fragmentation, with different user interfaces, policies, etc.
- For whatever reasons, many scholars do not bother to reposit their manuscripts in institution repositories.
- Even when mandates are in place, compliance is often miserable, to the point where Peter Suber considers the 80% NIH compliance rate as “respectable”. It really isn’t. 100% is acceptable; 99% is respectable.
- Many IRs have abject search facilities, often for example lacking the ability to restrict searches to papers that are actually available.
- Many IRs impose unnecessary restrictions on the use of the materials they contain: for example, Bath’s repo prohibits further redistribution.
- There is no central point for searching all IRs (at least not one that is half-decent; I know about OAIster).
- The quality of metadata within most IRs variable at best
- Use of metadata across IRs is inconsistent — hence many of the problems that render OAIster near-useless.
… and, I am sure, many more that I’ve not thought of right now.
Could these issues be addressed? Yes, probably; but ten years have unfortunately not done much to resolve them, so I don’t feel all that confident that the next ten will.
Do the IR advocates have a plan for solving these problems? Because they are much more political/sociological than technical, and those always seem to be the hardest ones to solve.